SMTL ID : 7s2y.1

SAMHD1 HD domain bound to CNDAC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x 85T: 4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one(Non-covalent)

85T.1: 17 residues within 4Å: Chain A: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:H.139, A:Y.298 Hydrogen bonds: A:Q.73, A:R.88, A:D.243, A:Y.298, A:Q.299 Water bridges: A:R.130, A:R.130, A:K.236, A:K.236 Salt bridges: A:R.88, A:R.130, A:H.134, A:H.157, A:H.157, A:K.236, A:R.290 85T.6: 17 residues within 4Å: Chain B: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:H.139, B:Y.298 Hydrogen bonds: B:Q.73, B:R.88, B:D.235, B:Y.239, B:D.243, B:Y.298, B:Q.299 Water bridges: B:R.130, B:R.130 Salt bridges: B:R.88, B:R.130, B:H.134, B:H.157, B:H.157, B:K.236, B:R.290 85T.12: 15 residues within 4Å: Chain C: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, Y.298, Q.299 Ligands: MG.15 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:L.74, C:Y.298 Hydrogen bonds: C:Q.73, C:R.88, C:D.235, C:Y.239, C:D.243, C:Q.299 Water bridges: C:R.130, C:R.130, C:R.130, C:R.130, C:R.130, C:R.130, C:H.139, C:H.139, C:N.304 Salt bridges: C:R.88, C:R.130, C:H.134, C:H.157, C:H.157, C:K.236, C:R.290 85T.19: 16 residues within 4Å: Chain D: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.20 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.74, D:Y.298 Hydrogen bonds: D:Q.73, D:R.88, D:D.243, D:Q.299 Water bridges: D:R.88, D:R.88, D:R.130, D:R.130, D:R.130, D:N.304 Salt bridges: D:R.88, D:R.130, D:H.134, D:H.157, D:H.157, D:K.236, D:R.290

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.2: 20 residues within 4Å: Chain A: R.257, F.261, R.276, K.278, N.282, K.447 Chain B: V.41, I.42, N.43, H.49 Chain C: V.80, F.81, P.82, I.249, R.296, H.300, K.301, V.302 Ligands: MG.9, GTP.11 20 PLIP interactions: 11 interactions with chain A, 7 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:R.257, A:N.282, A:N.282, B:N.43, B:N.43 Salt bridges: A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447, C:H.300, C:H.300, C:K.301, C:K.301, C:K.301 pi-Cation interactions: A:R.257, A:R.257 Hydrophobic interactions: C:V.80, C:F.81 DTP.7: 18 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, R.296, H.300, K.301, V.302 Ligands: MG.3, GTP.18 20 PLIP interactions: 11 interactions with chain B, 7 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.257, B:N.282, B:N.282, A:N.43, A:N.43 Salt bridges: B:R.257, B:R.276, B:K.278, B:K.278, B:K.278, B:K.447, D:H.300, D:H.300, D:K.301, D:K.301, D:K.301 pi-Cation interactions: B:R.257, B:R.257 Hydrophobic interactions: D:V.80, D:F.81 DTP.10: 20 residues within 4Å: Chain A: V.80, F.81, P.82, I.249, R.296, H.300, K.301, V.302 Chain C: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.41, I.42, N.43, H.49 Ligands: MG.14, GTP.16 23 PLIP interactions: 3 interactions with chain D, 13 interactions with chain C, 7 interactions with chain A Hydrogen bonds: D:N.43, D:N.43, C:R.257, C:N.282, C:N.282 Water bridges: D:K.40, C:R.276, C:R.276 Salt bridges: C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447, A:H.300, A:H.300, A:K.301, A:K.301, A:K.301 pi-Cation interactions: C:R.257, C:R.257 Hydrophobic interactions: A:V.80, A:F.81 DTP.17: 19 residues within 4Å: Chain B: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Chain C: V.41, I.42, N.43, H.49 Chain D: R.257, F.261, R.276, K.278, N.282, K.447 Ligands: GTP.5, MG.13 20 PLIP interactions: 7 interactions with chain B, 11 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:V.80, B:F.81 Salt bridges: B:H.300, B:H.300, B:K.301, B:K.301, B:K.301, D:R.257, D:R.276, D:K.278, D:K.278, D:K.278, D:K.447 Hydrogen bonds: D:R.257, D:N.282, D:N.282, C:N.43, C:N.43 pi-Cation interactions: D:R.257, D:R.257

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: K.40 Chain B: K.447 Ligands: DTP.7, GTP.18 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain A: R.130, D.233, K.236 Ligands: 85T.1 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.233, H2O.1, H2O.1 MG.8: 4 residues within 4Å: Chain B: R.130, S.226, D.233 Ligands: 85T.6 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.226, H2O.1, H2O.1, H2O.1 MG.9: 4 residues within 4Å: Chain A: K.447 Chain B: K.40 Ligands: DTP.2, GTP.11 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain C: K.40 Ligands: GTP.5, DTP.17 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain C: K.447 Chain D: K.40 Ligands: DTP.10, GTP.16 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: D.233, K.236 Ligands: 85T.12 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain D: D.233, K.236 Ligands: 85T.19 No protein-ligand interaction detected (PLIP)

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.5: 16 residues within 4Å: Chain B: Y.79, V.80, V.302, R.375, K.379 Chain C: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain D: K.447 Ligands: MG.13, DTP.17 14 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:R.375, C:V.41, C:Q.66, C:R.69 Salt bridges: B:R.375, B:K.379, B:K.379, C:K.40, C:K.40, C:K.40, C:D.61, D:K.447, D:K.447 pi-Cation interactions: B:R.375 GTP.11: 17 residues within 4Å: Chain A: K.447 Chain B: K.40, V.41, I.42, V.57, I.60, D.61, Q.66, R.69, F.89 Chain C: Y.79, V.80, V.302, R.375, K.379 Ligands: DTP.2, MG.9 15 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:K.40, B:V.41, B:Q.66, B:R.69, C:R.375 Salt bridges: B:K.40, B:K.40, B:K.40, B:D.61, C:R.375, C:K.379, C:K.379, A:K.447, A:K.447 pi-Cation interactions: C:R.375 GTP.16: 15 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375 Chain C: K.447 Chain D: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Ligands: DTP.10, MG.14 15 PLIP interactions: 9 interactions with chain D, 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: D:V.41, D:Q.66, D:R.69, A:R.375 Water bridges: D:K.40, D:K.40 Salt bridges: D:K.40, D:K.40, D:K.40, D:D.61, A:R.375, A:K.379, C:K.447, C:K.447 pi-Cation interactions: A:R.375 GTP.18: 17 residues within 4Å: Chain A: K.40, V.41, I.42, V.57, I.60, D.61, Q.66, R.69, F.89 Chain B: K.447 Chain D: Y.79, V.80, V.302, R.375, K.379 Ligands: MG.3, DTP.7 14 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B, 5 interactions with chain D Hydrogen bonds: A:V.41, A:Q.66, A:R.69, D:R.375 Salt bridges: A:K.40, A:K.40, A:K.40, A:D.61, B:K.447, B:K.447, D:R.375, D:K.379, D:K.379 pi-Cation interactions: D:R.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rothenburger, T. et al., Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells. J Exp Clin Cancer Res (2021)

Release Date

2021-10-27

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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